


Oh, how we miss him. Let us count the ways.

by Comixgal



Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe
Genre: Alpha/Beta/Omega Dynamics, Alternate Universe - Canon Divergence, F/M, M/M, Multi, Unresolved Romantic Tension, Unresolved Sexual Tension
Language: English
Status: Completed
Published: 2018-04-02
Updated: 2018-04-02
Packaged: 2019-04-17 01:32:48
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,394
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/14177676
Author URL: https://archiveofourown.org/users/Comixgal/pseuds/Comixgal
Summary: Omegas are rare - less than thirty percent of the population. They act like queens in a hive; bonding the alphas and betas around them into a cohesive unit.When Coulson is killed by Loki in the Hellicarrier, no one has time to process his loss. It’s felt, though, in a thousand tiny ways. Later, nobody, not even the Avengers, understands why they miss their bland, boring, beta handler so much.





	Oh, how we miss him. Let us count the ways.

Pepper, Bruce, and Rhodey were gathered in Bruce’s apartment. They all sighed happily at the pleasant lemony scent that pervaded the space. Near-silent air purifiers were working hard to keep all the anxious alpha pheromones out of the air.

The three betas were worn out. Keeping the alphas calm was becoming a near full-time job for the three of them. Pepper and Rhodey kept a close eye on Tony, their most fractious alpha. Bruce was closest to Natasha. All three tried to support Clint and Steve when they needed it.

“How did Phil do it?” Bruce asked, chewing listlessly on the granola he’d made earlier in the week.

“No idea.” Rhodey groaned, rotating his head on his neck, trying to loosen the tension. “It must have had to do with all the time he spent dealing with Hill and Fury. If you can keep those two calm, then you can handle anything. Also working with Natasha and Clint can’t have been easy.”

“We can’t keep this up.” Pepper said. She was already trying to plan her schedule for the next week. “Tony and Steve are going to fight one another for dominance soon if something doesn’t give. They keep arguing with each other.”

Bruce had irrationally hoped that Pepper and Rhodey hadn’t noticed the tension between the two alphas. There was no good outcome to this situation -- Either they would fight and one of them would win, or one of them had to leave. There was no guarantee that if Tony lost, he wouldn’t kick Steve out of the tower. They also knew that Steve was incapable of throwing the fight. It was more likely that Steve would leave the Avengers instead of fighting the man he both loved and hated.

“There’s nothing to fight _for_.” Rhodey said wearily. “We’re not a workable unit without an omega. What’s the point of fighting one another when we’re not a hive anyway?”

Pepper was nodding, “If the dominance fight triggers an alpha-heat in any of them, we’re going to have to quarantine the building. Stark Industries can’t afford that. Hell, the group can’t afford that.”

They sat in silence, contemplating the rare and dangerous phenomena that could send the alphas around them into a frenzy. Though the PC term was alpha-heat, they all knew it was a rut that turned even the most mild of alphas into insatiable hyper-sexual creatures. It could last days and required either complete seclusion and access to omega analogues (i.e. lots and lots of fuck toys) or a real omega to calm the alpha down.

“We can’t let that happen.” Bruce said as he levered himself from the couch. “I’ll go see if Steve wants to spend the evening together.”

Rhodey grimaced as he also stood. “I’ll check on Tony.”

“Let me know if he needs me.” Pepper offered. She knew that Rhodey wasn’t physically attracted to men.

“Or me.” Bruce said. “I’ll let you know whether I’m going to be with Steve.”

Rhodey smiled gratefully at both of them.

******

“Damnit, Tony! You can’t keep leaving your dirty dishes around! We’re not here to pick up after you!” Steve slammed down a pile of plates with barely restrained force.

“I never said you were! That’s what the robots are for!” Tony said from behind the freezer door.

“They don’t seem to be working.” Natasha growled, feeling irritable because both Tony and Steve were putting off too many pheromones. She envied Clint’s current sniper mission. The other alpha always seemed to be working away from the Tower these days.

“They’re shy. They don’t like working when others are around.” Tony’s voice heavily implied that both Steve and Natasha could leave if they wanted to.

Natasha’s muscles tensed and she bit down hard on her response.

“You invited us all here.” Bruce said softly from a corner of the room.

All three alphas startled - how long had the man been there?

Tony closed the freezer. “Yeah, well, that’s when I thought we might become a working hive.”

Both alphas and the beta went still.

“Are you kicking us out?” Bruce whispered, though the words seemed to fly directly into each of them.

Tony’s eyes went wide when he realized exactly what he’d said. “Oh god! No. Never! I mean, of course not! I didn’t mean it that way! I just--” He dropped his forehead against the wall. “It’s just all gone wrong since--” He didn’t complete the thought. They all knew what he was going to say.

_Since Coulson died_

“I’m going for a run.” Steve said.

Natasha flowed gracefully off the couch. “I’ll join you.”

Bruce stared at the genius alpha. The man looked like he was close to vibrating out of his skin.

“I’d never kick you out. I couldn’t. The building belongs to Pepper.”

Bruce nodded. He knew they’d made that decision so that a more level head controlled the housing of their dysfunctional hive.

“Steve just drives me crazy. I don’t know whether I want to fight him or fuck him.” Tony ran his hand through his hair.

Bruce silently began making a cup of tea.

“Fuck Coulson!” Tony slammed the cabinet. “Fuck him for dying! Fuck him for leaving! Fuck him for taking away our only omega!”

Bruce stared at him in stunned disbelief.

Tony stopped, shocked at his own words. He stared back at Bruce.

Holding on to his own calm, Bruce finished the two cups of tea and brought one to his friend and lover. When he finally spoke, it was almost too quiet for Tony to hear. “JARVIS, was Phil an omega?”

Whether it took a little while for his voice to reach the microphones or whether the A.I. didn’t know how to answer, Bruce would never know. JARVIS eventually responded almost as softly, “I believe that is a valid hypothesis.”

Bruce and Tony looked at one another. A tiny twitch of a smile flitted across Tony’s face.

“Do you think JARVIS said _hypothesis_ so that we’d move into science mode?” Bruce asked, also starting to smile.

“Analyze any biodata we have on him. That time he got drunk, the time he had a fever, bring up the elevator air analysis for every single fucking time he entered it. Isolate any times he rode alone. Find any scans that might have run when he came into my workshop. Analyze _**_EVERYTHING_**_.”

“Yes, sir.” JARVIS responded.

“His S.H.I.E.L.D. files didn’t say anything?” Bruce asked, alluding to the multiple times Tony had hacked into their database.

“Nothing.” Tony had grabbed up his Stark Pad and was already falling into full research mode.

Bruce followed the alpha into the lab. “JARVIS, copy the biodata to my workspace please. I want to run my own analysis.” He put on some headphones and soothing classical music immediately began playing. He looked up just once to see Tony gulp down his tea, grimace at the mug, then immediately forget about it as he started looking at the data.

******

“Coulson was an omega?!” Tony shouted at Maria Hill when she stopped by the Tower the following day.

Hill took a step back, hand on her holster, watching the wild-haired genius shake a Stark Pad in her face.

“He what?” Steve demanded. He reached out to take the Pad from Tony. He looked through the information, face growing darker and darker as he scrolled. He turned on Hill, “Coulson was an omega?”

“Oh shit. Of course he was.” Clint’s voice cracked with emotion as he walked into the kitchen, hair still wet from the shower he’d just taken after his most recent mission.

Maria rolled her eyes. “Why don’t you pull everyone together and we can chat about this. I’m not repeating myself.”

They all assembled in the room. Pepper sat with Tony. Bruce sat with Tony. Clint and Natasha stood side-by-side behind the couch wearing identical glares for Maria.

Tony spoke first. “Special Agent Phil Coulson: Omega, yes or no?”

“Yes.” Maria Hill said.

“And we weren’t told because…?” Pepper asked.

“Because it was Need-To-Know and you didn’t need to know.” Maria held out a hand to stall the inevitable arguments. “Fury hoped that Phil would bring you all together into a hive but we all agreed, Coulson included, that there was no point putting any unnecessary pressure on the team. We needed to you to save the world. Everything else was secondary.”

Steve was frowning at her. “It’s not secondary anymore.”

At nearly the same time, Natasha said, “Hiding his orientation benefits you more than it does us.”

Hill gave Steve a quick nod of agreement before frowning at the Black Widow, “My hive is perfectly functional, thank you very much. We don’t need another omega.”

Pepper grew angry, “Just how many omegas are being hidden in S.H.I.E.L.D.?”

“As many as are qualified to do the type of work we do and have a desire to do it. Just like alphas and betas.” Maria shot back. “We don’t discriminate.”

Bruce took a deep lungful of Maria’s scent, “Nick Fury, yourself, Jasper Sitwell, that tall doctor from medical -”

“Ranesh.” Maria supplied, blushing a bit.

“That annoying beta couple out of the sciences.” Tony added.

Pepper supplied these names, “Jemma and Leo. And you don’t like them because they’re almost as smart as you are and impervious to your charms.” She told Tony.

“Now we know why.” He shot back.

Bruce was still thinking, “Melinda May’s another alpha. Who is the omega?” 

“Victoria” “Tori” Steve and Clint said at the same time. 

Pepper smiled at them both before turning back to Maria. “Victoria Hand is an exceptional woman. So where the hell does that leave all of us?”

Hill shrugged. “The Avengers are still an active team. S.H.I.E.L.D. isn’t going to meddle in your personal lives.”

Only Natasha’s hand on Clint’s shoulder kept him from launching across the room to strangle Maria. “Get out. We loved him! We didn’t even get a chance to come together as a hive and here you are flaunting your status in front of us after telling us that the man we loved was an omega. Get out!”

Maria did leave, back straight and pretending she didn’t feel the stares of many very deadly humans following her.

Tony growled. “I need to get out of here too. I can’t stay in this Tower for another second.”

Pepper started to argue about his upcoming meetings. “Save it, Pep. I’ll call in from wherever I decide to stay. I’ll be back in a couple days.”

“Want company?” Bruce asked.

Tony’s eyes flicked between Bruce and Steve. He shook his head.

Both men pretended they didn’t smell the acrid mixture of desire, frustration, and shame that wafted between them.

Clint and Natasha still stood rigidly. With a small shake, Natasha looked around. “Well, I have some research I need to do, and some people I need to speak to.” She gripped Clint’s arm. “Don’t leave again without saying goodbye.”

Barton sighed. “Then I’ll say goodbye now. Every time I walk around here, it smells less like him. I hate it. I’m going back on assignment.”

Bruce’s throat tightened at this admission. “We miss you.” He reached out to Clint.

“I miss you too, wonderful.” Clint nuzzled Bruce’s neck. “But the longer Coulson’s gone, the more it hurts.”

Bruce frowned and nodded. “I know.” He let the sniper leave. He looked around at the others, his sensitive nose picking up so many unsaid things. “I’ll be in my lab. JARVIS, I’m going to need your help.”

******

No one saw Tony, Bruce, or Clint for five whole days. Without the tension between Steve and Tony, everyone was calmer. Pepper reported that Tony had dutifully conferenced in to the two meetings on his schedule and that he was at one of his private high-computing labs in the Canadian Rockies.

When Steve asked about Bruce, JARVIS would only say that the man was working on delicate research but had also been in contact with Tony.

The morning that Bruce came into the kitchen for breakfast, Steve smiled at him, “So you’re alive.”

Bruce’s laughter was a little wild and bordered on hysterical. Clint, Steve, and Natasha crowded around him. “Funny you should say that.” Bruce said as he wiped a hand over his face. “I- uh- I think Phil is still alive.”

The silence around him was deafening.

“Bru-”

He interrupted Clint. “Hear me out.” He took the man’s hand. “You’re the primary reason I think so.”

Clint’s eyes widened, strong grip spasming around Bruce’s fingers. Pheromones of shock and desperate, hopeless longing washed over them.

“You were bonded with him, even if you didn’t realize it. You spent so much time together. Coulson was grooming you to be in his hive. He wanted you to be one of his alphas. I could smell how close you two were when we first met. I thought it was because he was your handler.”

“It was.” Clint croaked.

“No.” Bruce pulled Clint down to sit next to him. “Knowing that he was-- is an omega makes so many things clearer. I never got to smell you before you met Coulson but your scent didn’t change the same way it would have if he’d actually died.”

Steve was gentle in his response, “Bruce, that could be because they weren’t bonded.”

The scientist smiled at him. “Do you really believe that? Knowing Phil and knowing Clint and how much they cared about one another, do you really believe that? Smell him. As Phil’s scent fades, you can get the base scent. Think about it. Think about how they smelled when they were working together. Don’t you see? They had at least pre-bonded.”

Natasha, who had been still until that point, pulled away. “He’s right. I could smell it when you brought me in. And I could smell it on myself as I joined you. It’s the reason I stayed. You were so close and you invited me in. Phil invited me in.”

Clint looked between them all. “But- I mean - but that doesn’t mean anything. He’s still gone.” His voice was unsteady. “I can’t get my hopes up.”

“Clint, listen to me, I need you to hear me on this; the science is with me. I’m certain you were at least pre-bonded and your scent didn’t change the way it would have if Coulson had died. That bond isn’t just pheromonal. He’s still alive. Whether it means he’s in a coma or something, I don’t know, but I think he’s alive. And so does Tony. I’ve got him searching for proof.”

Steve pulled Clint close to him, letting the man sag against his chest. “Alright, Bruce. I believe you. What should we do?”

Having an alpha on-board and taking charge unconsciously relaxed the beta. “We need to wait for Tony’s information. I need to sleep. We’ll know more soon.”

He padded out of the room, breakfast forgotten.

Clint dropped into a chair. “Shit.” He shook his head. “I can’t let myself believe this. Even if he’s alive, what if he’s hurt? What if he’s paralyzed or in a coma? Why else would he have left us alone for so long? If he loves me, why hasn’t he come back?”

Nat spun away from them. “Well, I have to believe it. And I have to believe in Tony’s ability to find him.” She began walking away.

Steve groaned. Both other alphas looked at him. “This means Tony is hacking into S.H.I.E.L.D. again.” He sighed. “I do wish Fury would stop trying to hide information from us. At this point, that sneaky bastard deserves this.”

Clint and Nat laughed at the description. It eased the tension in the room.

With a deep sigh, Clint stood up. “I’m going to get Tony’s address out of Pepper and go bring him home.”

That sounded like a great idea to them, so Natasha and Steve let him go.

******

Tony flew into the room where Steve and Natasha were playing a game of chess. “They’re moving him! Or they have moved him. We have to go get him!”

Natasha nearly hurled the pointy end of a bishop at Tony’s head.

“Slow down, Tony! You’re not making sense.” Steve said. “And welcome back, by the way.”

“JARVIS found proof that Phil was released from a rehab hospital yesterday. We have to go find him! We have to bring him home!” Tony brought up a holographic map. It showed a car zipping away from a nondescript building. “Satellites lost the car about an hour from here but I’ve got JARVIS working on it and he’ll have a location for us soon. We need to be ready to go.”

Steve tried to sound reasonable. “Tony, we can’t just assemble the team to try follow up an unsubstantiated lead.”

“It’s not unsubstantiated! I am telling you that I’ve found Phil. We need to go get him!” He began pacing.

“And we will.” Steve soothed. “Once JARVIS has a new location we’ll make a plan.”

“I have a plan, Cap! My plan is to get into my suit and be ready the moment we have a location!”

“Tony-” Steve was cut off when the other male alpha turned and shook a Stark Pad in his face.

“I’m telling you we need to go!”

Steve reached out instinctively to grab Tony’s arms while Natasha plucked the pad out of his hands. Tony tried to pull away, face growing darker.

“Stop that.”

All three alphas froze. They knew that voice. Steve dropped his hands from Tony’s wrists and took a step back.

A near palpable wave preceded the steady and measured steps that brought Phil Coulson into the room. Six eyes followed him as he made his way first to Natasha.

Phil reached up to grasp his former asset’s shoulder. His lips twitched in a small smile when either Steve or Tony whimpered behind them.

Nat mirrored the grasp, “Welcome back.” They all registered the sudden lightness in her scent as it blended with Coulson’s. “You smell like Clint.” She whispered.

He grinned, “I saw him before coming here.”

“Awww, he’s your favourite.” She tugged at his collar. “That explains the hickey.”

Phil blushed and turned to the two men. Steve was staring at him in shock, tears streaming down his face while Tony had collapsed into a chair and curled in on himself. Phil gave Steve a reassuring nod before reaching towards the smaller man. “Tony, come here.” He helped pull Tony up from the chair. “I hear you’ve been making life difficult for Bruce.” He teased gently.

“Have not!” The alpha insisted, burying his head against Phil’s neck and inhaling deeply.

“Pepper too, I’ll bet.” He kissed Tony’s temple. “Try not to antagonize our betas, okay love?”

All three alphas sighed at the easy declaration of the betas as theirs. They were so close to being a full hive. Tony’s scent mixed with that of Clint, Nat, and Phil and he relaxed enough to be set back down on the chair.

“Steven.” Coulson held out his arms. “I’ve missed you.”

Steve stepped into them, still crying. A sour odor assaulted them as their scents mixed, making the large man sob harder.

“Shhhhhhhh.” Phil soothed, gripping strongly to keep Steve from pulling away. “You’re trying too hard. You’re mine. You belong to us. Let go. We love you. We _all_ love you.”

Tony came up behind Phil to wrap his arms around the omega and pull Steve closer. At Tony’s touch, their scents melded seamlessly. Steve lifted his head from where it had been resting against Phil’s and was immediately kissed by Tony.

When they pulled apart, Phil reached up to wipe away the last of Steve’s tears. “That’s good, my sweet alpha. You’ll take care of us. You’ve got your entire team together and safe. It’s been hard on you, I know. And when we find Bucky, he can join us too if he wants. We’re going to be a hive and I’m not going to go anywhere.”

“Phil-” Bruce’s soft voice was harsh with emotion.

The three alphas spun, having missed the entrance of the betas.

Pepper kept her eyes on Phil as she went first to Steve and then to Tony, checking on them out of instinct. Bruce had navigated to Natasha. When they’d checked on the alphas, they converged on Phil. Rhodey stayed back a bit, watching things play out.

Phil turned to the the distant man. “James. I’m sorry it took me so long. You don’t have to stay.”

Rhodey gave a sad but relieved smile.

“Send us wedding invitations when a date is set.” Pepper said from her spot next to Tony.

“I will.” He saluted Phil and Steve then turned and left.

The pheromones within the room continued to merge until they all felt as if they were bathed in the soothing scent of their omega’s claim.

Coulson moved constantly around the room, touching each person, kissing them, rubbing a hand over their necks. He turned to the door just before it opened.

Clint’s laughing eyes surveyed them all. “Started without me.”

“Says our omega’s primary.” Natasha teased back.

Both Clint and Phil grinned like children, faces turning red. Clint gravitated to Phil’s side and pulled the man close. The omega relaxed against his archer’s chest with a sigh.

“I’ll let S.H.I.E.L.D., Stark Industries, and one of the other super-teams know that we’re going to be out of commission for a few days.” Pepper said as she levered herself up from between Steve and Tony.

“What? Why? We --” Tony stopped abruptly as he caught a new scent in the air. “Oh.”

Phil was not at all ashamed. “We have a day or two before it really starts.”

Clint nipped at the man’s neck. “Enough time to get you settled and set up a room with all your favorites.”

“You’re my favorites.” Coulson said through a breathless moan.

Bruce laughed. “Favorite foods and drinks.”

“And toys!” Tony got up. “I have some stuff to do in the lab! Don’t start without me!” He paused and sobered, looking at everyone. He pulled into himself a little, “Seriously, though, please don’t start without me. Please?”

Steve hugged him close, “We won’t, Tony. Promise. You’re important to the hive. You can be the second alpha through the door. Okay?” Steve checked over his shoulder to make sure Phil approved.

Everyone in the room was nodding.

“Don’t make us come get you.” Pepper warned. “When JARVIS says it’s time, don’t keep the rest of us waiting.”

“Promise!” Tony waved as he headed out of the room.

“You’d better! Or I’m sending Natasha to drag your ass up the stairs!” Pepper shouted after him.

Nat smiled languidly at the idea. She was sitting with her legs across Bruce’s lap and her back against the couch arm. Every time Phil passed by her, he kissed her hands. Bruce was beaming at them all, clearly thrilled by today’s outcome.

“You’re going to need the special condoms.” Clint said, pulling the scientist out of his thoughts.

“What? Why?” Bruce reddened when he realized he was echoing Tony.

“Phil is going to want everyone involved.” Clint said. “Betas too. You should have your special condoms on hand.”

Bruce looked over at Phil.

“He’s right.” The omega said. “Clint’s absolutely right.” He looked at each alpha, “The betas will be active participants in my heat. I don’t feel that there’s any other way for the hive to come together properly.”

“We have no idea how gamma irradiated semen could affect you.” Bruce said. “It’s best if I take a peripheral role.”

“Hence the special condoms.” Clint clarified. “This isn’t negotiable, Bruce. You’re joining us for the heat and you’re taking part. Your orgasm pheromones need to be part of the hive’s scent.”

Coulson stood in front of Bruce and pulled him up off the couch. “Clint says you’re the reason they didn’t give up on me. He says you convinced them all that I was still alive.”

Bruce nodded, unable to form a response.

“Thank you.” Coulson pulled him into a deep kiss. “Thank you, thank you, thank you. I don’t know what I would have done if I’d returned to find that my alphas had abandoned the hive.”

It was Bruce’s turn to cry. He clung to the solidly built man. “I thought I was wrong. I thought I might be getting their hopes up and that you’d never come back. I thought Tony and Steve would fight and that we’d never come together. I thought-” his next words were lost in a sob.

“I know, my beta. I know.” Phil soothed. “I’m sorry I put you through that. I hope you’ll forgive me.” He let Bruce cling tighter. “After this heat, you’ll do some research and figure out if you can forego the condoms next time, okay? I need you there, my brilliant, loving beta who has taken such good care of the team. I need you there because I love you and you’re mine.”

“I love you too.” Bruce let Coulson pass him off to Steve who was holding a tissue and a bottle of water.

“I’m sorry I put all of you through that. I hope you’ll let me explain.”

“Eventually.” Pepper said in her I-run-this-company voice as she came back into the room. “For right now, it really doesn’t matter. We need to make sure you’re set up for our Bonding and we’re all going to be hyper-focused on you for the next few days.” She obviously thought about Tony’s disappearance into his labs. “In our own ways.” She added a little weakly.

Even Bruce gave a watery chuckle at this.

“Clint and Bruce will make sure your rooms are exactly as you’d like, I’ll make sure our schedules are clear, and Steve and Natasha will be responsible for ensuring the security of the buildings and suites. Your only job is to find one-on-one time with each of us and plan the Bonding itself. Alright?”

Phil kissed her cheek. “Thank you, dearest. I’ll check in on everyone until it’s time.”

Clint had already led Bruce away. Phil reach out for Natasha. “Come tell me everything I’ve missed.”

With a happy sigh Nat followed him.


End file.
